The mutation–selection process is the most fundamental mechanism of evolution. In 1935, R. A. Fisher proved his fundamental theorem of natural selection, providing a model in which the rate of change of mean fitness is equal to the genetic variance of a species. Fisher did not include mutations in his model, but believed that mutations would provide a continual supply of variance resulting in perpetual increase in mean fitness, thus providing a foundation for neo-Darwinian theory. In this paper we re-examine Fisher’s Theorem, showing that because it disregards mutations, and because it is invalid beyond one instant in time, it has limited biological relevance. We build a differential equations model from Fisher’s first principles with mutations added, and prove a revised theorem showing the rate of change in mean fitness is equal to genetic variance plus a mutational effects term. We refer to our revised theorem as the fundamental theorem of natural selection with mutations. Our expanded theorem, and our associated analyses (analytic computation, numerical simulation, and visualization), provide a clearer understanding of the mutation–selection process, and allow application of biologically realistic parameters such as mutational effects. The expanded theorem has biological implications significantly different from what Fisher had envisioned.

There is hardly any aspect of our lives that is not profoundly influenced by water. From climate to commerce and agriculture to health, water shapes our physical environment, regulates the major energy exchanges that determine climate on Earth, and is the matrix that supports the physical and chemical processes of life as we know it (1). The chemistry and physics of water, which underlie all of its uses, its necessity for life, its effects on other molecules and on the environment, are very active areas of research at the present time. So, why is this? Surprisingly, there are major gaps in knowledge and understanding that persist despite this substance’s ubiquity and central importance. This Special Feature on the Chemical Physics of Water contains 10 articles and aims to be a representative cross-section of current frontier research in this field. Articles include both Perspectives and original research contributions. The pioneering paper by Bernal and Fowler dealing with the chemical physics of water appeared in 1933 (2). It focused on understanding the anomalous properties of water and its ionic solutions from a molecular perspective, inspired by the newly minted quantum mechanical theory of electronic structure. Since that time, theory and computer simulation have become established as essential complements to laboratory experiments in unraveling the crucial role of water in an array …

↵1To whom correspondence may be addressed. Email: pdebene@princeton.edu or mike.klein@temple.edu.

by Robert J Marks II (Author),‎ William A Dembski (Author),‎ Winston Ewert (Author)

Science has made great strides in modeling space, time, mass and energy. Yet little attention has been paid to the precise representation of the information ubiquitous in nature.

Introduction to Evolutionary Informatics fuses results from complexity modeling and information theory that allow both meaning and design difficulty in nature to be measured in bits. Built on the foundation of a series of peer-reviewed papers published by the authors, the book is written at a level easily understandable to readers with knowledge of rudimentary high school math. Those seeking a quick first read or those not interested in mathematical detail can skip marked sections in the monograph and still experience the impact of this new and exciting model of nature's information.

This book is written for enthusiasts in science, engineering and mathematics interested in understanding the essential role of information in closely examined evolution theory.

Readership: General/Popular; Enthusiasts in science, engineering and apologetics and to those interested in the information theoretic components of closely examined evolution.

Editorial Reviews

Review

An honest attempt to discuss what few people seem to realize is an important problem. Thought provoking! -- Gregory Chaitin "Professor, Federal University of Rio de Janeiro, Brazil"

With penetrating brilliance, and with a masterful exercise of pedagogy and wit, the authors take on Chaitin's challenge, that Darwin's theory should be subjectable to a mathematical assessment and either pass or fail. Surveying over seven decades of development in algorithmics and information theory, they make a compelling case that it fails. -- Bijan Nemati "Jet Propulsion Laboratory, California Institute of Technology, USA"

Introduction to Evolutionary Informatics is a lucid, entertaining, even witty discussion of important themes in evolutionary computation, relating them to information theory. It's far more than that, however. It is an assessment of how things might have come to be the way they are, applying an appropriate scientific skepticism to the hypothesis tha -- Donald Wunsch "Distinguished Professor and Director of the Applied Computational Intelligence Lab, Missouri University of Science & Technology, USA"

Darwinian pretensions notwithstanding, Marks, Dembski, and Ewert demonstrate rigorously and humorously that no unintelligent process can account for the wonders of life. -- Michael J Behe "Professor of Biological Sciences, Lehigh University, USA"

A very helpful book on this important issue of information. Information is the jewel of all science and engineering which is assumed but barely recognised in working systems. In this book Marks, Dembski and Ewert show the major principles in understanding what information is and show that it is always associated with design. -- Andy C McIntosh "Visiting Professor of Thermodynamics, School of Chemical and Process Engineering, University of Leeds, LEEDS, UK"

Though somewhat difficult, Marks, Dembski and Ewert have done a masterful job of making the book accessible to the engaged and thoughtful layperson. I could not endorse this book more highly. -- J P Moreland "Distinguished Professor of Philosophy, Biola University, USA"

This is an important and much needed step forward in making powerful concepts available at an accessible level. -- Ide Trotter "Trotter Capital Management Inc., Founder of the Trotter Prize & Endowed Lecture Series on Information, Complexity and Inference (Texas A&M, USA)"

This is a fine summary of an extremely interesting body of work. It is clear, well-organized, and mathematically sophisticated without being tedious (so many books of this sort have it the other way around). It should be read with profit by biologists, computer scientists, and philosophers. -- David Berlinski "David Berlinski"

Evolution requires the origin of new information. In this book, information experts Bob Marks, Bill Dembski, and Winston Ewert provide a comprehensive introduction to the models underlying evolution and the science of design. The authors demonstrate clearly that all evolutionary models rely implicitly on information that comes from intelligent desi -- Jonathan Wells "Senior Fellow, Discovery Institute"

Introduction to Evolutionary Informatics helps the non-expert reader grapple with a fundamental problem in science today: We cannot model information in the same way as we model matter and energy because there is no relationship between the metrics. As a result, much effort goes into attempting to explain information away. The authors show, using c -- Denyse O'Leary, Science Writer "Denyse O'Leary, Science Writer" --This text refers to the Hardcover edition.

About the Author

Robert J Marks II is Distinguished Professor of Engineering in the Department of Engineering at Baylor University, USA. Marks's professional awards include a NASA Tech Brief Award and a best paper award from the American Brachytherapy Society for prostate cancer research. He is Fellow of both IEEE and The Optical Society of America. His consulting activities include: Microsoft Corporation, DARPA, and Boeing Computer Services. He is listed as one of the "The 50 Most Influential Scientists in the World Today." By TheBestSchools.org. (2014). His contributions include: the Zhao-Atlas-Marks (ZAM) time-frequency distribution in the field of signal processing, and the Cheung Marks theorem in Shannon sampling theory.

Marks's research has been funded by organizations such as the National Science Foundation, General Electric, Southern California Edison, the Air Force Office of Scientific Research, the Office of Naval Research, the United States Naval Research Laboratory, the Whitaker Foundation, Boeing Defense, the National Institutes of Health, The Jet Propulsion Lab, Army Research Office, and NASA. His books include Handbook of Fourier Analysis and Its Applications (Oxford University Press), Introduction to Shannon Sampling and Interpolation Theory (Springer Verlag), and Neural Smithing: Supervised Learning in Feedforward Artificial Neural Networks (MIT Press) with Russ Reed. Marks has edited/co-edited five other volumes in fields such as power engineering, neural networks, and fuzzy logic. He was instrumental in defining the discipline of computational intelligence (CI) and is a co-editor of the first book using CI in the title: Computational Intelligence: Imitating Life (IEEE Press, 1994). His authored/coauthored book chapters include nine papers reprinted in collections of classic papers. Other book chapters include contributions to Michael Arbib's The Handbook of Brain Theory and Neural Networks (MIT Press, 1996), and Michael Licona et al.'s Evidence for God (Baker Books, 2010), Marks has also authored/co-authored hundreds of peer-reviewed conference and journal papers.

William A Dembski is Senior Research Scientist at the Evolutionary Informatics Lab in McGregor, Texas; and also Senior Fellow with Seattle's Discovery Institute, Washington, USA. He holds a BA in Psychology, MS in Statistics, PhD in Philosophy, and a PhD in Mathematics (awarded in 1988 by the University of Chicago, Chicago, Illinois, USA), and an MDiv degree from Princeton Theological Seminary (1996, New Jersey, USA). Dembski's work experience includes being an Associate Research Professor with the Conceptual Foundations of Science, Baylor University, Waco, Texas, USA. He has taught at Northwestern University, Evanston, Illinois, USA; the University of Notre Dame, Notre Dame, Indiana, USA; and the University of Dallas, Irving, Texas, USA. He has done postdoctoral work in mathematics with the Massachusetts Institute of Technology, Cambridge, USA; in physics with the University of Chicago, USA; and in computer science with Princeton University, Princeton, New Jersey, USA. He is a Mathematician and Philosopher. He has held National Science Foundation graduate and postdoctoral fellowships, and has published articles in mathematics, engineering, philosophy, and theology journals and is the author/editor of more than twenty books.

Winston Ewert is currently a Software Engineer in Vancouver, Canada. He is a Senior Research Scientist at the Evolutionary Informatics Lab. Ewert holds a PhD from Baylor University, Waco, Texas, USA. He has written a number of papers relating to search, information, and complexity including studies of computer models purporting to describe Darwinian evolution and developing information theoretic models to measure specified complexity.

Edited by David C. Page, Whitehead Institute, Cambridge, MA, and approved July 19, 2016 (received for review January 8, 2016)

Significance

Much of our understanding of the chronology of human evolution relies on a fixed “molecular clock”; that is, a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole-genome sequences from 10 primate species. We find that there is substantial variation in the molecular clock between apes and monkeys and that rates even differ within hominines. Importantly, not all mutation types behave similarly; notably, transitions at CpG sites exhibit a more clocklike behavior than other substitutions, presumably because of their nonreplicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions.

Abstract

Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid–NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years,​ and the human and gorilla divergence time is 15.1 million years​.

Although the concept of structural water that is bound inside hydrophobic pockets and helps to stabilize protein structures is well established, water has rarely found a similar role in supramolecular polymers. Water is often used as a solvent for supramolecular polymerization, however without taking the role of a comonomer for the supramolecular polymer structure. We report a low–molecular weight monomer whose supramolecular polymerization is triggered by the incorporation of water. The presence of water molecules as comonomers is essential to the polymerization process. The supramolecular polymeric material exhibits strong adhesion to surfaces, such as glass and paper. It can be used as a water-activated glue, which can be released at higher temperatures and reused many times without losing its performance.

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

• The proposed method allows to evaluate spatial capillary area and central line independently on properties of individual capillary.

• Simultaneous blood flow velocity records related to a few neighbor capillaries into a capillary net are demonstrated for the first time.

Source/Fonte: Igor Gurov

Abstract

The video capillaroscopy system with high image recording rate to resolve moving red blood cells with velocity up to 5 mm/s into a capillary is considered. Proposed procedures of the recorded video sequence processing allow evaluating spatial capillary area, capillary diameter and central line with high accuracy and reliability independently on properties of individual capillary. Two-dimensional inter frame procedure is applied to find lateral shift of neighbor images in the blood flow area with moving red blood cells and to measure directly the blood flow velocity along a capillary central line. The developed method opens new opportunities for biomedical diagnostics, particularly, due to long-time continuous monitoring of red blood cells velocity into capillary. Spatio-temporal representation of capillary blood flow is considered. Experimental results of direct measurement of blood flow velocity into separate capillary as well as capillary net are presented and discussed.

Why do most academic fields, and science in particular, have such significant gender and racial imbalances? This so-called “leaky pipeline,” where women disproportionately leave scientific and academic careers, is well documented; but the role played by sexual and racial harassment in this process has received little attention. Sexual misconduct is prevalent in any industry where men hold a disproportionate amount of power and women are systematically underrepresented; academia and science are no different. Women in science are therefore not surprised by the scale and scope of recent reports of sexual misconduct by powerful men in politics, in the media, and in Hollywood, because so many of us have our own stories of sexual harassment. Additionally, women of color also encounter racial harassment—a double jeopardy that the current moment of reckoning with sexual misconduct has not addressed with equivalent rigor and reflection. To address and root out the rampant sexual and racial harassment in science we must enact individual, institutional and policy changes.

Why We Are Long Overdue for a Reckoning

Almost every woman in science has either personally experienced or knows someone who has experienced sexual harassment or assault. In our broader society, the recent resurgence of Tarana Burke’s “Me Too" movement has illustrated just how prevalent and deep-rooted these issues are. In science and academia, as a result of women speaking out and journalists reporting concrete evidence, many egregious stories of alleged sexual harassment and assault have recently been brought to light. The stories are barely the tip of the iceberg—an iceberg of sexual harassers in science and academia floating in an ocean of enablers supported by a system that is all too willing to look away. How many victims of such harassment have been driven out of science as a result? What contributions to science have been lost?

In addition to individual stories, there have been scientific surveys and studies of harassment in science and academia. In a remarkable study, Clancy et al. recently surveyed 474 astronomers and planetary scientists on their experiences with sexism and racism in the last five years. They found that harassment and assault were more prevalent for women of color, who reported feeling unsafe in the workplace as a result of their gender or sex 40 percent of the time, and as a result of their race 28 percent of the time.

Their study quantified the fact that women of color, in addition to having to deal with sexual harassment, have to deal with racism; this cannot be neglected in our larger conversation about sexual misconduct. They also found that 18 percent of women of color and 12 percent of white women lost career opportunities because they did not feel safe attending events where they experienced harassment by other colleagues. Another Clancy study in 2014 found that 64 percent of scientists engaged in fieldwork had experienced sexual harassment and 20 percent sexual assault. Sexism and racism are alive and well in science and are likely strong contributors to the leaky pipeline.

If so many women in science have personally been subject to harassment or worse, why aren’t more women openly talking about it and naming their offenders? The answer is surprisingly straightforward: victims do not hold the power and therefore live in fear of retaliation. In the academic and scientific world, this retaliation can hamstring the necessary ingredients for a successful career: interfering with a victim’s grant funding, preventing publication of peer-reviewed articles, and negatively impacting a victim’s job opportunities, which in small and insular academic fields are heavily reliant on formal and informal confidential recommendations.

Retaliation can be effective because of the entrenched hierarchy of the overwhelmingly white, male academic network and its outsized influence. Adding to the danger of direct retaliation, accusations from women who speak out are often dismissed as false or worse; the women who speak out have to live with the professional consequences of being an accuser and being labeled as someone difficult to work with. One such instance of retaliation was recently highlighted by Sarah Gossan.

As a way to cope with the imbalance of power, many women are forced to resort to whisper networks, sharing the names of offenders and institutes that willingly harbor them. But many young women don’t get access to this kind of information until it is too late, and these networks are never 100 percent effective against preventing harassment. Even with access to information, we can never truly prepare for the experience of being harassed and the professional aftermath. What do you do if you are a young graduate student presenting a poster at a major conference and a famous older man in the field you hope is impressed by your work is instead more interested in staring at your chest? What if this older man follows you to your hotel, or even worse, up to your room? What if your harasser is your thesis supervisor, a person who has the power to destroy your career? What if your harasser happens to be your supervisor and you are working at a remote field site, where you’re stuck for weeks or months? What if your harasser is an academic peer, and the authorities refuse to take action to save your harasser’s career from ruin? Is his career more important and valuable than yours? The manifestation of the existing power structure, where we have to weigh our careers and professional reputations against our health and safety is deeply unfair; we must shift the burden of those decisions and their consequences onto those with the power, not the victims. ...

• Design heuristics can help designers explore alternative concepts in early conceptual design.

How do product designers create multiple concepts to consider? To address this question, we combine evidence from four empirical studies of design process and outcomes, including award-winning products, multiple concepts for a project by an experienced industrial designer, and concept sets from 48 industrial and engineering designers for a single design problem. This compilation of over 3450 design process outcomes is analyzed to extract concept variations evident across design problems and solutions. The resulting set of patterns, in the form of 77 Design Heuristics, catalog how designers appear to introduce intentional variation into conceptual product designs. These heuristics provide ‘cognitive shortcuts’ that can help designers generate more, and more varied, candidate concepts to consider in the early phases of design.

DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely related populations. Close examination of one signal, an increased TCC

→TTC mutation rate in Europeans, indicates a burst of mutations from about 15,000 to 2000 years ago, perhaps due to the appearance, drift, and ultimate elimination of a genetic modifier of mutation rate. Our results suggest that mutation rates can evolve markedly over short evolutionary timescales and suggest the possibility of mapping mutational modifiers.

DNA is a molecule that contains the information needed to build an organism. This information is stored as a code made up of four chemicals: adenine (A), guanine (G), cytosine (C), and thymine (T). Every time a cell divides and copies its DNA, it accidentally introduces ‘typos’ into the code, known as mutations. Most mutations are harmless, but some can cause damage. All cells have ways to proofread DNA, and the more resources are devoted to proofreading, the less mutations occur. Simple organisms such as bacteria use less energy to reduce mutations, because their genomes may tolerate more damage. More complex organisms, from yeast to humans, instead need to proofread their genomes more thoroughly.

Recent research has shown that humans have a lower mutation rate than chimpanzees and gorillas, their closest living relatives. Humans and other apes copy and proofread their DNA with basically the same biological machinery as yeast, which is about a billion years old. Yet, humans and apes have only existed for a small fraction of this time, a few million years. Why then do humans need to replicate and proofread their DNA differently from apes, and could it be that the way mutations arise is still evolving?

Previous research revealed that European people experience more mutations within certain DNA motifs (specifically, the DNA sequences ‘TCC’, ‘TCT’, ‘CCC’ and ‘ACC’) than Africans or East Asians do.

Now, Harris (who conducted the previous research) and Pritchard have compared how various human ethnic groups accumulate mutations and how these processes differ in different groups.

Statistical analysis of the genomes of thousands of people from all over the world did indeed show that the mutation rates of many different three-letter DNA motifs have changed during the past 20,000 years of human evolution. Harris and Pritchard report that when groups of humans left Africa and settled in isolated populations across different continents, each population quickly became better at avoiding mutations in some genomic contexts, but worse in others. This suggests that the risk of passing on harmful mutations to future generations is changing and evolving at an even faster rate than was originally suspected.

The results suggest that every human ethnic group carries specific variants of the genes which ensure that DNA replication and repair are accurate. These differences appear to influence which types of mutations are frequently passed down to future generations. An important next step will be to identify the genetic variants that could be controlling mutational patterns and how they affect human health.

We searched for positional brain surface asymmetries measured as displacements between corresponding vertex pairs in relation to a mid-sagittal plane in Magnetic Resonance (MR) images of the brains of 223 humans and 70 chimpanzees. In humans deviations from symmetry were observed: 1) a Torque pattern comprising right-frontal and left-occipital “petalia” together with downward and rightward “bending” of the occipital extremity, 2) leftward displacement of the anterior temporal lobe and the anterior and central segments of superior temporal sulcus (STS), and 3) posteriorly in the position of left occipito-temporal surface accompanied by a clockwise rotation of the left Sylvian Fissure around the left-right axis. None of these asymmetries was detected in the chimpanzee, nor was associated with a sex difference. However, 4) an area of cortex with its long axis parallel to the olfactory tract in the orbital surface of the frontal lobe was found in humans to be located higher on the left in females and higher on the right in males. In addition whereas the two hemispheres of the chimpanzee brain are equal in extent in each of the three dimensions of space, in the human brain the left hemisphere is longer (p = 3.6e-12), and of less height (p = 1.9e-3), but equal in width compared to the right. Thus the asymmetries in the human brain are potential correlates of the evolution of the faculty of language.

The human brain contains roughly 100 billion neurons, which are organized into complex networks. But how does the brain establish these networks in the first place? Neurons have long projections known as axons and, in the developing brain, these axons form structures called growth cones at their tips. The growth cones possess finger-like appendages that probe their surroundings in search of signals displayed on the surface of other cells. These signals guide the growth cones to their targets and move the axon tip into a position where it can form connections with other neurons within a particular network.

The signals that growth cones follow are often distributed in concentration gradients so that the levels of a signal may be low at one end of a brain structure and gradually increase to a maximum level at the other end. In the developing visual system, for example, about one million axons from the retina reach their proper targets in visual regions of the brain by reading gradients of signals called ephrins and Ephs. However, when Fiederling et al. studied retinal neurons in a petri dish, they found that the axons became much less sensitive to both signals upon prolonged exposure to them. This unexpected finding raised a new question. If neurons rely upon these gradients for navigation, how do they continue to find their way if they also become less sensitive to those signals over time?

Fiederling et al. used a computer to simulate the events occurring in the developing brain. The simulations were based on the idea that navigating growth cones sense the ratio of ephrins to Ephs, instead of sensing the individual concentrations of these signals. Thus, by keeping the amounts of all involved sensors in strict proportion to each other while continuously re-adjusting them, the axons could still be accurately guided to their targets even though the neurons would become less sensitive to the signals. Experiments in neurons grown in petri dishes confirmed that retinal growth cones do exactly this and regulate the amounts of ephrin and Eph sensors on their outer membranes in a highly coordinated manner using a previously unknown mechanism.

Given that signaling requires energy, the brain may have evolved this system to reduce the costs associated with wiring itself up. The system also offers greater flexibility than guidance based on the absolute concentrations of the signals. If other regions of the brain use a similar mechanism to establish their own wiring patterns, then understanding such basic mechanisms might eventually provide insights into diseases of miswiring such as schizophrenia and autism.